The primary goal of the recently renamed Functional Genomics and Microbiome Core (Core C) is to enhance research programs in infection and injury states affecting the mammalian intestine and liver by providing genomics and metagenomics expertise and resources. In this Core, we utilize advanced technology in mammalian and microbial genomics to support ongoing and innovative research to prevent and cure digestive diseases. This Core enables investigators to posit research questions related to gene expression, functional genomics and molecular mechanisms by utilizing the tools of microarrays, deep nucleic acid sequencing (microbial and mammalian), nucleic acid amplification, protein profiling, and bioinformatics. PCR based analyses of gene expression and splicing, DNA mutation/SNP detection, and gene pathway analyses ofthe mammalian metagenome (microbe and man) will be fostered by this Core as a platform for gastrointestinal and hepatic systems biology. Our mission is to provide a full service resource from experimental design to consultations about specimen processing, robust data analysis pipelines, and biostatistical support. In summary, we have created a fully integrated genomic analysis platform for investigators studying digestive diseases.